HEADER LYASE 13-MAR-02 1L6S TITLE CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE TITLE 2 INHIBITOR 4,7-DIOXOSEBACIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DELTA-AMINOLEVULINIC ACID DEHYDRATASE, 5-AMINOLEVULINIC ACID COMPND 5 DEHYDRATASE; COMPND 6 EC: 4.2.1.24; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDRATASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR E.K.JAFFE,J.KERVINEN,J.MARTINS,F.STAUFFER,R.NEIER,A.WLODAWER,A.ZDANOV REVDAT 6 16-OCT-24 1L6S 1 REMARK REVDAT 5 16-AUG-23 1L6S 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1L6S 1 VERSN REVDAT 3 24-FEB-09 1L6S 1 VERSN REVDAT 2 01-OCT-02 1L6S 1 JRNL REVDAT 1 17-APR-02 1L6S 0 JRNL AUTH E.K.JAFFE,J.KERVINEN,J.MARTINS,F.STAUFFER,R.NEIER, JRNL AUTH 2 A.WLODAWER,A.ZDANOV JRNL TITL SPECIES-SPECIFIC INHIBITION OF PORPHOBILINOGEN SYNTHASE BY JRNL TITL 2 4-OXOSEBACIC ACID JRNL REF J.BIOL.CHEM. V. 277 19792 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11909869 JRNL DOI 10.1074/JBC.M201486200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.KERVINEN,E.K.JAFFE,F.STAUFFER,R.NEIER,A.WLODAWER,A.ZDANOV REMARK 1 TITL MECHANISTIC BASIS FOR SUICIDE INACTIVATION OF REMARK 1 TITL 2 PORPHOBILINOGEN SYNTHASE BY 4,7-DIOXOSEBACIC ACID, AN REMARK 1 TITL 3 INHIBITOR THAT SHOWS DRAMATIC SPECIES SELECTIVITY REMARK 1 REF BIOCHEMISTRY V. 40 8227 2001 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI010656K REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 126253 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 12122 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4916 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 497 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015696. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1I8J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, 10% GLYCEROL, 0.1M TRIS-HCL, REMARK 280 PH 8.5, 0.02% SODIUM AZIDE, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS AN OCTAMER REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 46560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 75030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -380.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 129.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 64.50000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 64.50000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 -64.50000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 64.50000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 4 CG1 CG2 CD1 REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 HIS A 135 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 LYS A 320 CG CD CE NZ REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 4 CG1 CG2 CD1 REMARK 470 LYS B 12 CG CD CE NZ REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 HIS B 135 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 212 CG CD CE NZ REMARK 470 LYS B 320 CG CD CE NZ REMARK 470 ARG B 323 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 39 OE2 GLU A 39 8666 1.53 REMARK 500 OE2 GLU B 39 OE2 GLU B 39 8665 1.67 REMARK 500 O HOH A 640 O HOH A 733 4455 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 39 CB GLU A 39 CG 0.124 REMARK 500 GLU B 39 CB GLU B 39 CG 0.136 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 129 45.45 -77.72 REMARK 500 ALA A 210 46.48 -79.20 REMARK 500 TYR A 218 -56.16 -133.90 REMARK 500 LYS A 320 28.53 44.89 REMARK 500 GLU B 39 50.06 38.93 REMARK 500 CYS B 129 38.77 -71.97 REMARK 500 ALA B 210 43.08 -73.95 REMARK 500 TYR B 218 -47.53 -136.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 218 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 ATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE REMARK 600 TO NZ OF LYS246 AND NZ OF LYS194. REMARK 600 THE OXYGENS ON THE C4 AND C7 ARE ELIMINATED REMARK 600 DURING THIS REACTION. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 119 SG REMARK 620 2 CYS A 121 SG 120.4 REMARK 620 3 CYS A 129 SG 99.4 113.7 REMARK 620 4 HOH A 685 O 104.9 96.8 123.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 231 OE1 REMARK 620 2 HOH A 403 O 90.1 REMARK 620 3 HOH A 422 O 79.5 87.7 REMARK 620 4 HOH A 433 O 171.1 83.1 94.5 REMARK 620 5 HOH A 439 O 94.0 169.0 83.0 91.7 REMARK 620 6 HOH A 483 O 88.1 93.7 167.5 97.9 96.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 119 SG REMARK 620 2 CYS B 121 SG 123.4 REMARK 620 3 CYS B 129 SG 102.2 109.2 REMARK 620 4 HOH B 686 O 106.1 90.0 128.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 231 OE1 REMARK 620 2 HOH B 412 O 85.1 REMARK 620 3 HOH B 421 O 172.5 87.7 REMARK 620 4 HOH B 427 O 92.8 94.1 89.6 REMARK 620 5 HOH B 430 O 92.6 177.6 94.6 86.5 REMARK 620 6 HOH B 448 O 81.4 90.6 96.7 172.3 88.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSB A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSB B 350 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I8J RELATED DB: PDB REMARK 900 1I8J CONTAINS PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR REMARK 900 4,7-DIOXOSEBACIC ACID REMARK 900 RELATED ID: 1L6Y RELATED DB: PDB REMARK 900 1L6Y CONTAINS PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR REMARK 900 4-OXOSEBACIC ACID DBREF 1L6S A 1 323 UNP P0ACB2 HEM2_ECOLI 1 323 DBREF 1L6S B 1 323 UNP P0ACB2 HEM2_ECOLI 1 323 SEQADV 1L6S CME A 133 UNP P0ACB2 CYS 133 MODIFIED RESIDUE SEQADV 1L6S CME B 133 UNP P0ACB2 CYS 133 MODIFIED RESIDUE SEQRES 1 A 323 THR ASP LEU ILE GLN ARG PRO ARG ARG LEU ARG LYS SER SEQRES 2 A 323 PRO ALA LEU ARG ALA MET PHE GLU GLU THR THR LEU SER SEQRES 3 A 323 LEU ASN ASP LEU VAL LEU PRO ILE PHE VAL GLU GLU GLU SEQRES 4 A 323 ILE ASP ASP TYR LYS ALA VAL GLU ALA MET PRO GLY VAL SEQRES 5 A 323 MET ARG ILE PRO GLU LYS HIS LEU ALA ARG GLU ILE GLU SEQRES 6 A 323 ARG ILE ALA ASN ALA GLY ILE ARG SER VAL MET THR PHE SEQRES 7 A 323 GLY ILE SER HIS HIS THR ASP GLU THR GLY SER ASP ALA SEQRES 8 A 323 TRP ARG GLU ASP GLY LEU VAL ALA ARG MET SER ARG ILE SEQRES 9 A 323 CYS LYS GLN THR VAL PRO GLU MET ILE VAL MET SER ASP SEQRES 10 A 323 THR CYS PHE CYS GLU TYR THR SER HIS GLY HIS CYS GLY SEQRES 11 A 323 VAL LEU CME GLU HIS GLY VAL ASP ASN ASP ALA THR LEU SEQRES 12 A 323 GLU ASN LEU GLY LYS GLN ALA VAL VAL ALA ALA ALA ALA SEQRES 13 A 323 GLY ALA ASP PHE ILE ALA PRO SER ALA ALA MET ASP GLY SEQRES 14 A 323 GLN VAL GLN ALA ILE ARG GLN ALA LEU ASP ALA ALA GLY SEQRES 15 A 323 PHE LYS ASP THR ALA ILE MET SER TYR SER THR LYS PHE SEQRES 16 A 323 ALA SER SER PHE TYR GLY PRO PHE ARG GLU ALA ALA GLY SEQRES 17 A 323 SER ALA LEU LYS GLY ASP ARG LYS SER TYR GLN MET ASN SEQRES 18 A 323 PRO MET ASN ARG ARG GLU ALA ILE ARG GLU SER LEU LEU SEQRES 19 A 323 ASP GLU ALA GLN GLY ALA ASP CYS LEU MET VAL LYS PRO SEQRES 20 A 323 ALA GLY ALA TYR LEU ASP ILE VAL ARG GLU LEU ARG GLU SEQRES 21 A 323 ARG THR GLU LEU PRO ILE GLY ALA TYR GLN VAL SER GLY SEQRES 22 A 323 GLU TYR ALA MET ILE LYS PHE ALA ALA LEU ALA GLY ALA SEQRES 23 A 323 ILE ASP GLU GLU LYS VAL VAL LEU GLU SER LEU GLY SER SEQRES 24 A 323 ILE LYS ARG ALA GLY ALA ASP LEU ILE PHE SER TYR PHE SEQRES 25 A 323 ALA LEU ASP LEU ALA GLU LYS LYS ILE LEU ARG SEQRES 1 B 323 THR ASP LEU ILE GLN ARG PRO ARG ARG LEU ARG LYS SER SEQRES 2 B 323 PRO ALA LEU ARG ALA MET PHE GLU GLU THR THR LEU SER SEQRES 3 B 323 LEU ASN ASP LEU VAL LEU PRO ILE PHE VAL GLU GLU GLU SEQRES 4 B 323 ILE ASP ASP TYR LYS ALA VAL GLU ALA MET PRO GLY VAL SEQRES 5 B 323 MET ARG ILE PRO GLU LYS HIS LEU ALA ARG GLU ILE GLU SEQRES 6 B 323 ARG ILE ALA ASN ALA GLY ILE ARG SER VAL MET THR PHE SEQRES 7 B 323 GLY ILE SER HIS HIS THR ASP GLU THR GLY SER ASP ALA SEQRES 8 B 323 TRP ARG GLU ASP GLY LEU VAL ALA ARG MET SER ARG ILE SEQRES 9 B 323 CYS LYS GLN THR VAL PRO GLU MET ILE VAL MET SER ASP SEQRES 10 B 323 THR CYS PHE CYS GLU TYR THR SER HIS GLY HIS CYS GLY SEQRES 11 B 323 VAL LEU CME GLU HIS GLY VAL ASP ASN ASP ALA THR LEU SEQRES 12 B 323 GLU ASN LEU GLY LYS GLN ALA VAL VAL ALA ALA ALA ALA SEQRES 13 B 323 GLY ALA ASP PHE ILE ALA PRO SER ALA ALA MET ASP GLY SEQRES 14 B 323 GLN VAL GLN ALA ILE ARG GLN ALA LEU ASP ALA ALA GLY SEQRES 15 B 323 PHE LYS ASP THR ALA ILE MET SER TYR SER THR LYS PHE SEQRES 16 B 323 ALA SER SER PHE TYR GLY PRO PHE ARG GLU ALA ALA GLY SEQRES 17 B 323 SER ALA LEU LYS GLY ASP ARG LYS SER TYR GLN MET ASN SEQRES 18 B 323 PRO MET ASN ARG ARG GLU ALA ILE ARG GLU SER LEU LEU SEQRES 19 B 323 ASP GLU ALA GLN GLY ALA ASP CYS LEU MET VAL LYS PRO SEQRES 20 B 323 ALA GLY ALA TYR LEU ASP ILE VAL ARG GLU LEU ARG GLU SEQRES 21 B 323 ARG THR GLU LEU PRO ILE GLY ALA TYR GLN VAL SER GLY SEQRES 22 B 323 GLU TYR ALA MET ILE LYS PHE ALA ALA LEU ALA GLY ALA SEQRES 23 B 323 ILE ASP GLU GLU LYS VAL VAL LEU GLU SER LEU GLY SER SEQRES 24 B 323 ILE LYS ARG ALA GLY ALA ASP LEU ILE PHE SER TYR PHE SEQRES 25 B 323 ALA LEU ASP LEU ALA GLU LYS LYS ILE LEU ARG MODRES 1L6S LYS A 246 LYS SCHIFF BASE LINKAGE MODRES 1L6S LYS A 194 LYS SCHIFF BASE LINKAGE MODRES 1L6S LYS B 246 LYS SCHIFF BASE LINKAGE MODRES 1L6S LYS B 194 LYS SCHIFF BASE LINKAGE MODRES 1L6S CME A 133 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 1L6S CME B 133 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 133 10 HET CME B 133 10 HET ZN A 400 1 HET MG A 401 1 HET DSB A 350 14 HET ZN B 400 1 HET MG B 401 1 HET DSB B 350 14 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM DSB 4,7-DIOXOSEBACIC ACID FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 DSB 2(C10 H14 O6) FORMUL 9 HOH *497(H2 O) HELIX 1 1 ARG A 6 LYS A 12 5 7 HELIX 2 2 SER A 13 GLU A 21 1 9 HELIX 3 3 SER A 26 ASN A 28 5 3 HELIX 4 4 HIS A 59 ALA A 70 1 12 HELIX 5 5 GLY A 88 ARG A 93 5 6 HELIX 6 6 GLY A 96 VAL A 109 1 14 HELIX 7 7 ASP A 138 GLY A 157 1 20 HELIX 8 8 GLY A 169 ALA A 181 1 13 HELIX 9 9 TYR A 200 GLY A 208 1 9 HELIX 10 10 ASN A 224 GLN A 238 1 15 HELIX 11 11 TYR A 251 GLU A 260 1 10 HELIX 12 12 VAL A 271 ALA A 284 1 14 HELIX 13 13 ASP A 288 ALA A 303 1 16 HELIX 14 14 PHE A 312 LYS A 319 1 8 HELIX 15 15 ARG B 6 LYS B 12 5 7 HELIX 16 16 SER B 13 PHE B 20 1 8 HELIX 17 17 SER B 26 ASN B 28 5 3 HELIX 18 18 HIS B 59 ALA B 70 1 12 HELIX 19 19 GLY B 88 ARG B 93 5 6 HELIX 20 20 GLY B 96 VAL B 109 1 14 HELIX 21 21 ASP B 138 ALA B 156 1 19 HELIX 22 22 GLY B 169 ALA B 181 1 13 HELIX 23 23 TYR B 200 GLY B 208 1 9 HELIX 24 24 ASN B 224 GLN B 238 1 15 HELIX 25 25 TYR B 251 GLU B 260 1 10 HELIX 26 26 VAL B 271 ALA B 284 1 14 HELIX 27 27 ASP B 288 ALA B 303 1 16 HELIX 28 28 PHE B 312 LYS B 319 1 8 SHEET 1 A 7 ALA A 187 ILE A 188 0 SHEET 2 A 7 PHE A 160 PRO A 163 1 N ILE A 161 O ALA A 187 SHEET 3 A 7 ILE A 113 THR A 118 1 N SER A 116 O PHE A 160 SHEET 4 A 7 SER A 74 ILE A 80 1 N THR A 77 O MET A 115 SHEET 5 A 7 LEU A 30 GLU A 37 1 N ILE A 34 O MET A 76 SHEET 6 A 7 MET A 53 PRO A 56 1 O ILE A 55 N GLU A 37 SHEET 7 A 7 LYS A 44 ALA A 45 -1 N LYS A 44 O ARG A 54 SHEET 1 B 9 ALA A 187 ILE A 188 0 SHEET 2 B 9 PHE A 160 PRO A 163 1 N ILE A 161 O ALA A 187 SHEET 3 B 9 ILE A 113 THR A 118 1 N SER A 116 O PHE A 160 SHEET 4 B 9 SER A 74 ILE A 80 1 N THR A 77 O MET A 115 SHEET 5 B 9 LEU A 30 GLU A 37 1 N ILE A 34 O MET A 76 SHEET 6 B 9 LEU A 307 SER A 310 1 O SER A 310 N VAL A 31 SHEET 7 B 9 ILE A 266 GLN A 270 1 N GLN A 270 O PHE A 309 SHEET 8 B 9 LEU A 243 LYS A 246 1 N LEU A 243 O GLY A 267 SHEET 9 B 9 THR A 193 LYS A 194 1 N THR A 193 O MET A 244 SHEET 1 C 7 ALA B 187 ILE B 188 0 SHEET 2 C 7 PHE B 160 PRO B 163 1 N ILE B 161 O ALA B 187 SHEET 3 C 7 ILE B 113 THR B 118 1 N SER B 116 O PHE B 160 SHEET 4 C 7 SER B 74 ILE B 80 1 N VAL B 75 O MET B 115 SHEET 5 C 7 LEU B 30 GLU B 37 1 N ILE B 34 O MET B 76 SHEET 6 C 7 MET B 53 PRO B 56 1 O ILE B 55 N GLU B 37 SHEET 7 C 7 LYS B 44 ALA B 45 -1 N LYS B 44 O ARG B 54 SHEET 1 D 9 ALA B 187 ILE B 188 0 SHEET 2 D 9 PHE B 160 PRO B 163 1 N ILE B 161 O ALA B 187 SHEET 3 D 9 ILE B 113 THR B 118 1 N SER B 116 O PHE B 160 SHEET 4 D 9 SER B 74 ILE B 80 1 N VAL B 75 O MET B 115 SHEET 5 D 9 LEU B 30 GLU B 37 1 N ILE B 34 O MET B 76 SHEET 6 D 9 LEU B 307 PHE B 309 1 O ILE B 308 N VAL B 31 SHEET 7 D 9 ILE B 266 TYR B 269 1 N ALA B 268 O PHE B 309 SHEET 8 D 9 LEU B 243 LYS B 246 1 N LEU B 243 O GLY B 267 SHEET 9 D 9 THR B 193 LYS B 194 1 N THR B 193 O MET B 244 LINK C LEU A 132 N CME A 133 1555 1555 1.32 LINK C CME A 133 N GLU A 134 1555 1555 1.34 LINK NZ LYS A 194 C7 DSB A 350 1555 1555 1.28 LINK NZ LYS A 246 C4 DSB A 350 1555 1555 1.29 LINK C LEU B 132 N CME B 133 1555 1555 1.33 LINK C CME B 133 N GLU B 134 1555 1555 1.33 LINK NZ LYS B 194 C7 DSB B 350 1555 1555 1.29 LINK NZ LYS B 246 C4 DSB B 350 1555 1555 1.29 LINK SG CYS A 119 ZN ZN A 400 1555 1555 2.43 LINK SG CYS A 121 ZN ZN A 400 1555 1555 2.51 LINK SG CYS A 129 ZN ZN A 400 1555 1555 2.39 LINK OE1 GLU A 231 MG MG A 401 1555 1555 2.14 LINK ZN ZN A 400 O HOH A 685 1555 1555 2.26 LINK MG MG A 401 O HOH A 403 1555 1555 2.19 LINK MG MG A 401 O HOH A 422 1555 1555 2.24 LINK MG MG A 401 O HOH A 433 1555 1555 2.00 LINK MG MG A 401 O HOH A 439 1555 1555 2.06 LINK MG MG A 401 O HOH A 483 1555 1555 2.10 LINK SG CYS B 119 ZN ZN B 400 1555 1555 2.33 LINK SG CYS B 121 ZN ZN B 400 1555 1555 2.51 LINK SG CYS B 129 ZN ZN B 400 1555 1555 2.49 LINK OE1 GLU B 231 MG MG B 401 1555 1555 2.11 LINK ZN ZN B 400 O HOH B 686 1555 1555 2.57 LINK MG MG B 401 O HOH B 412 1555 1555 2.17 LINK MG MG B 401 O HOH B 421 1555 1555 2.10 LINK MG MG B 401 O HOH B 427 1555 1555 2.13 LINK MG MG B 401 O HOH B 430 1555 1555 2.08 LINK MG MG B 401 O HOH B 448 1555 1555 2.32 CISPEP 1 LYS A 246 PRO A 247 0 -0.32 CISPEP 2 LYS B 246 PRO B 247 0 -0.78 SITE 1 AC1 4 CYS A 119 CYS A 121 CYS A 129 HOH A 685 SITE 1 AC2 6 GLU A 231 HOH A 403 HOH A 422 HOH A 433 SITE 2 AC2 6 HOH A 439 HOH A 483 SITE 1 AC3 4 CYS B 119 CYS B 121 CYS B 129 HOH B 686 SITE 1 AC4 6 GLU B 231 HOH B 412 HOH B 421 HOH B 427 SITE 2 AC4 6 HOH B 430 HOH B 448 SITE 1 AC5 14 SER A 164 LYS A 194 PHE A 199 TYR A 200 SITE 2 AC5 14 PHE A 203 ARG A 204 ARG A 215 GLN A 219 SITE 3 AC5 14 LYS A 246 TYR A 269 VAL A 271 SER A 272 SITE 4 AC5 14 TYR A 311 HOH A 463 SITE 1 AC6 16 SER B 164 TYR B 191 LYS B 194 PHE B 199 SITE 2 AC6 16 TYR B 200 PHE B 203 ARG B 204 ARG B 215 SITE 3 AC6 16 GLN B 219 LYS B 246 TYR B 269 VAL B 271 SITE 4 AC6 16 SER B 272 TYR B 311 HOH B 511 HOH B 686 CRYST1 129.000 129.000 142.800 90.00 90.00 90.00 P 4 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007754 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007002 0.00000